This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This is a two phase project with the first being the optimization of label-free protein quantification for detecting differentially expressed proteins in a transgenic mouse model of breast cancer. The second phase is to use the quantification model to discover novel breast cancer effected proteins. Both phases will use the standard LC-MS/MS platform in use with the proteomics core, but will use statistical experimental design and a novel application of linear mixed models for data analysis.